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revision 1.765 by jmc, Fri Jan 12 19:18:24 2007 UTC revision 1.916 by dimitri, Mon Dec 3 07:45:27 2007 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/exf: added CPP option EXF_SUBTRACT_UVVEL_FROM_UVWIND for subtracting
8      UVEL and VVEL from UWIND and VWIND prior to applying bulk formulae.
9    
10    checkpoint59k
11    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
12      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
13    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
14      all experiments pass when compile with un-initilised var. checking option.
15    o added pkg/salt_plume
16    o script to test restart (for now, in MITgcm_contrib/jmc_script)
17    o pkg/seaice: new read/write pickup version.
18      read meta file and write only fields which are needed to restart.
19      ( same logic as main pickup file ; also using pickupStrictlyMatch )
20    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
21    o lab_sea.hb87: modify the domain & update output.hb87.txt :
22      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
23      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
24      process. Fixed here by closing the domain at the Northern boundary.
25    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
26    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
27      a set of consecutive levels in/from a 3-D array.
28    o pkg/ptracers:
29      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
30      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
31    
32    checkpoint59j
33    o in pkgs: dic, obcs, offline, rbcs:
34      standard way to compute coeff. for time interpolation between 2 time reccords
35      which retains full precision (& make results less dependent on compiler).
36      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
37    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
38      packages instead of reading ice cover and wind speed separately
39    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
40     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
41      to allow to compile customized code before the update)
42    o cleaning-up:
43      - fix CPP instruction syntax in pkg/obcs
44      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
45        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
46      - fix some threads issue in IO parts.
47    o pkg/dic:
48      - add tons of "_d 0" (--> much better testreports !)
49       and then update outputs of tutorial_global_oce_biogeo
50    o pkg/mom_fluxform:
51      add a special version of momentum advection intended to conserve momentum
52      next to a bathymetry step or a coastline edge. (default = off = #undef)
53    o new read/write pickup version:
54      - for now, only implemented for main (mdsio) pickup file.
55      - write out only what is needed to restart; merge pickup_nh , pickup_ph
56        and main pickup together.
57      - read meta file; read only what is needed to restart; stop if a field
58        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
59        if it make sense (even if the restart is not perfect).
60      - if no meta file, assume that pickup to read corresponds exactly to
61        a pickup that would currently be written.
62      - read pickup written in the old format (until checkpoint59i) if it
63        recognizes an old meta file (no field-list).
64      - add a meta file in exp. which starts from a pickup: 2 cases:
65        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
66         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
67        b) a meta file describing the content of the associated pickup file
68         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
69    o pkg/mdsio & pkg/rw:
70      - new routine to read a meta file ; new set of routine to read
71        Multiple-fields file (with meta file).
72    o added open boundary conditions capability for seaice
73        HSNOW, HSALT, UICE, and VICE
74    
75    checkpoint59i
76    o adjoint:
77      * fix multiDimAdvection adjoint
78        (partial recomputation problem by TAF for fVerT(:,:,kDown)
79        and comlev1 size definition (maxpass vs. max. number of tracers)
80      * verification/global_ocean.90x45x15 adjoint now tests
81        NLFS and multiDimAdvection using DST3 (=30)
82      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
83    o pkg/kpp: add "_d 0" to real constant (if missing);
84      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
85      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
86    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
87      for internal parameters related to restart process (formerly from PARAMS.h)
88      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
89    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
90      as argument. (only atm2d & obcs write_pickup have not yet been updated)
91    o pkg/monitor:
92      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
93      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
94      - account for deep Atmosphere factor and density factor (anelastic)
95    o added open boundary conditions capability for seaice HEFF and AREA
96    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
97      thermodynamics
98      - requires a little reorganization, which affects the testreport results
99        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
100        so that now the conservative form is tested
101      - add a few comments
102    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
103    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
104    o add new diagnostics to seaice: advective, diffusive fluxes (only for
105      multidim-advection, for scheme 2 they are not filled) and transports,
106      thermodynamic growth rates
107    o change units of EmPmR (inside the code, + within coupling interface)
108      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
109      Affects results @ truncation level (cg2d match) and update output of
110       experiments: lab_sea(6), global_ocean.90x40x15(10),
111      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
112      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
113      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
114      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
115    
116    checkpoint59h
117    o pkg/exf:
118      - improve vectorization by moving if-statement out of loops in
119        exf_mapfields, exf_radiation
120      - exf_bulkformulae.F: introduce 2D fields and vectorize code
121    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
122    o testreport:
123      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
124        monitor & update offline_exf_seaice exp. output.
125      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
126    o pkg/seaice:
127      - bug fix in the evp solver: boundary conditions were affected be
128        masking of zMax/zMin (changes results)
129      - minor bug fix in boundary conditions in seaice_calc_strainrates
130        (changes results for no_slip)
131      - seaice_lsr.F: make interpolation of eta dependent on boundaries
132      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
133      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
134        stress formulation and no-slip boundary conditions
135    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
136      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
137    o pkg/seaice: a first HSALT time stepping equation has been checked in
138    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
139      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
140      without requiring DO-IF statements
141    o pkg/thsice:
142      use continuous power-law function for partition of energy between lateral
143      melting/freezing and thinning/thickening ; old code using step function
144      still available with #undef THSICE_FRACEN_POWERLAW
145      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
146    o testreport: change AD testing : check against results/output_adm.txt
147      using same scripts as for forward test.
148    
149    checkpoint59g
150    o adjoint testing: in preparation for changing testreport:
151      - output format: cost and grad written on separated lines
152      - ad output results in directory "results" (instead of "results_ad")
153    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
154    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
155    o pkg/ecco: allow user defined cost function contributions
156    o testreport:
157      Allow to choose (per experiment) the list of tested output variables
158       and the main variable (used to issue a pass/FAIL ) ;
159      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
160      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
161      Also modify printing of summary:
162       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
163       b) echo the list of tested variables in the individual summary.txt of
164          each experiment.
165    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
166      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
167      (but still depend on the tile decompostion of the domain).
168    o pkg/seaice: change a discretization detail to make the B-grid code
169      "more symmetric". This change is likely to remove all "ridges/leads" that
170      where quasi-aligned with the grid in B-grid solutions. It may also be
171      the solution to the stress coupling issues with the B-grid.
172    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
173      remove .cvsignore from input dir. (since testreport no longer run here).
174    o pkg/thsice:
175     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
176     - fix reshaping of sea-ice just after advection:
177       melt all the ice only if ice-volume is too small.
178     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
179       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
180     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
181    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
182      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
183    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
184      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
185      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
186      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
187      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
188      -> update output.txt
189    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
190     this affects truncation error: -> update output.txt of exp:
191      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
192      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
193    
194    checkpoint59f
195    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
196    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
197      a bounded range (in forward mode)
198    o pkg/ecco, ctrl, autodiff and mom_common:
199     internal parameter controls, completements of implementations
200    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
201    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
202      (not seem any difference in testing results).
203    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
204       at face corners.
205    o pkg/generic_advdiff:
206     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
207      loop range indices for computing vertical advection tendency
208      and do the calculation in the interior only (no overlap) ;
209      for now, only implemented for SOM advection (to save CPU time).
210     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
211    o exch2 adjoint
212      First set of changes:
213      - add exch2 hand-written adjoint templates
214      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
215        This will require cleanup in pkg/autodiff/*.F
216        (changed routines currently kept separate in verif. code/)
217      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
218        that used to hide exch2 or cubed-sphere specific code
219        (commented via 'cph-exch2')
220    o pkg/seaice
221      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
222    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
223       output of global_ocean.cs32x15.thsice .
224    
225    checkpoint59e
226    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
227      for B-grid vector (not yet tested) and C-grid vector (<- only used
228      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
229    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
230      (#ifdef ALLOW_SALT_PLUME)
231    o gather_2d/scatter_2d: removed halo regions
232    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
233      scheme and the corresponding test case (under front_relax dir). For now,
234      only available with Skew-flux form and not yet tested in realistic set-up.
235      adjoint: store directives updated, but gradient checks deteriorated,
236      so maybe GM/Redi adjoint is now broken.
237    o seaice adjoint
238      * add AREA, HEFF, HSNOW as control variable
239        (should not change lab_sea results)
240      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
241    o pkg/seaice:
242      * added computation of saltFlux in seaice_growth;
243        For time being, sea ice salinity is assumed constant
244        contribution of snow flooding to freshening of sea ice is neglected.
245        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
246        defaults to 0.0 in order to maintain backward compatibility.
247        Typical values for SEAICE_salinity are 4 to 10 g/kg.
248      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
249      * added SEAICE_availHeatFrac, which specifies fraction of surface level
250        heat content used to melt or grow ice
251      * commented out cap of HICE: it helps keep ice thinner
252      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
253      * applied OBCS T/S mask to HEFFM sea ice mask
254    
255    checkpoint59d
256    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
257     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
258     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
259    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
260     and change default value of parameter "GM_Small_Number";
261     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
262       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
263       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
264    o pkg/ecco: cost function when applying pkg/smooth to controls
265    o pkg/ctrl: add forcingPrecond run time parameter
266    o pkg/seaice:
267     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
268     - fix bug in metric terms of u-equation in LSR solver (implicit part),
269       changes verification/lab_sea
270     - rearrange implicit part of u-equation in LSR solver to make it easier to
271       read, understand, and debug. This causes changes at the truncation level.
272     - fix (serious) bug in the boundary conditions (sign error in the implicit
273       part) of the LSR solver. Changes all LSR results.
274     - fixed problem with HSNOW initialization to avoid thick snow when AREA
275       is initilized with small values - does not change lab_sea results.
276     - added HsnowFile initialization capability
277    o pkg/smooth: addition to model/src and pkg/ctrl so allow
278     initialization of pkg/smooth and application to control vector
279    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
280    o dependencies: pkg/profiles requires pkg/cal
281    o pkg/profiles:
282     - added option ALLOW_PROFILES_GENERICGRID
283         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
284         that interpolation information (grid points and coefficients) is provided
285         within the netcdf input files.
286         -> sample matlab scripts can be found in MITgcm_contrib/gael
287         that allow you to prepare netcdf input files.
288     - also modified: cleaner include statements, cleaner error print statements,
289       cleaner stops when error, and more tests of the netcdf input files consistency.
290    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
291    o pkg/seaice:
292     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
293       requires a new routine: seaice_diagnostics_fill.F
294     - make sure that seaice does not move if not forced (pressure replacement
295       method, Hibler and Ip, 1995), changes results
296     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
297     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
298       It is turned off by default (=-1.), because it changes the results.
299     - make it possible to read AREA from a file, too.
300    
301    checkpoint59c
302    o add S/R and diagnostics for oceanic mixed-layer depth
303    o move GMRedi call after all vertical mixing schemes (including KPP)
304    o pkg/thsice:
305     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
306      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
307    o pkg/obcs:
308     - bug fix for balance code
309    o pkg/seaice:
310      - allow values of SEAICE_elasticParm > 1
311      - add new parameter SEAICE_evpTauRelax as an alternative
312        to SEAICE_elasticParm
313      - make lsr boundary conditions free slip (by default), changes result
314      - add code for no slip boundary conditions for lsr
315      - set minimum of zeta to zero (and not 4e8) (changes results)
316      - add a cap on AREA after advecting AREA if seaice_growth is not called
317    o change calculation of Visbeck K:
318      - no longer depend on tapering scheme; instead, compute slope (limited
319        by GM_maxSlope). this is equivalent to what was comuted before with
320        clipping or linear tappering.
321      - fix vertical averaging (wrong by 1/2 level)
322      - leave the old version (but will not be maintained) within
323        #ifdef OLD_VISBECK_CALC / #endif
324      - update output of exp. ideal_2D_oce
325    o change error catch in calc_r_star to improve vectorization
326    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
327      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
328    o adjoint:
329      Re-organized adjoint checkpointing according to Matt Mazloff
330      (but with modifs/completions/cleanups)
331      Storing is now bundled into large arrays to optimized I/O
332      (and second step in cleanup of the_main_loop)
333    
334    checkpoint59b
335    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
336      - export/import (between ocean & coupler) fields needed for ocean DIC.
337    o pkg/seaice:
338      - get rid of three more exchanges seaice_calc_viscosities (required
339        different loop boundaries in seaice_lsr and seaice_ocean_stress)
340      - bug fix in seaice_ocean_stress (update of lab_sea required)
341      - reduce loop boundaries to necessary minimum also in seaice_evp
342      - go back to the old way of computing deltaC/Z as the adjoint likes that
343        better
344    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
345      passive tracer to an Age Tracer) + update output.txt
346    o pkg/exf:
347      - implement A-grid / C-grid selection for wind-stress input files.
348      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
349      for now, in exf_bulk_largeyeager04.F only :
350      - change implementation for case where windspeed + 2. components wind-stress
351        are read-in. AND use rhoConstFresh to convert evap.
352    o pkg/seaice:
353      - use correct EXCH_UV for wind-forcing (on A-grid).
354      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
355        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
356    o pkg/exf:
357      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
358      EXF_INTERPOLATION:
359      - merge global_with_exf/code version of exf_interp_read.F
360        to the main code ;
361      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
362        reading the file ; Important: This options needs to be defined to recover
363        previous code.
364        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
365      - no longer loose real*8 precision along the way when using exf_iprec=64.
366    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
367      - change discretisation of evp-solver in order to avoid another exchange
368        (changes lab_sea) and clean up a little
369      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
370        help the adjoint (this also changes the results slightly)
371      - add a few "_d 0" where they had been missing in seaice_evp.F
372      - cleaning up: remove unused seaice_calc_rhs.F
373    o pkg/exf: some cleaning-up:
374      - change various "constants" into runtime parameters
375      - cleaned-up Large&Yeager04 routine which should eventually
376        replace exf_bulkformulae.F (changed names of S/R and CPP)
377        and merged various ALLOW_ATM_WIND options
378     only used with thsice pkg (in thsice_get_exf.F):
379      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
380        which are used when useStabilityFct_overIce=TRUE (= the default)
381      - change default values of ice & snow emissivity and scale downward LW
382        by ice & snow emissivity.
383    o pkg/thsice:
384     fix few little problems, in thsice_calc_thickn.F:
385      - growth vertically (and not laterally) if iceFrac == iceMaskMax
386      - melt only laterally if hIce < hThinIce (as the comments say)
387      and in thsice_extend.F:
388      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
389      - start to form ice as soon as the minimum ice-volume is reachable.
390     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
391      and cpl_aim+ocn
392    o pkg/kpp
393     - move computation of surface related input fields to KPP into a new
394       subroutine kpp_forcing_surf.F
395     - remove wrong (within bi,bj loops) EXCH calls.
396     - little cleaning (add argument myThid in last position, cvs header ...)
397     - for now, fix conservation problem by exchanging KPPviscAz (may not
398       be the best fix)
399    o pkg/seaice
400     - check for inconsistent evp parameter/cpp-flag combination
401     - remove leftover errIO flat for obsolete name list error handling
402    o OpenAD
403     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
404    
405    checkpoint59a
406    o pkg/seaice: some parameter clarifications and a little bit of clean up
407    o pkg/thsice: rename run-time parameters:
408       himin       -> hIceMin
409       himin0      -> hThinIce
410       hihig       -> hThickIce
411       i0          -> i0swFrac
412       transCoef   -> bMeltCoef
413       frac_energy -> fracMelting
414      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
415       with default values (for now) that do not change the results.
416      remove old version of thsice vars advection in pkg/seaice.
417    o in FFIELDS.h:
418      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
419      - make pLoad & sIceLoad always available (but still only used if
420         ATMOSPHERIC_LOADING is #define).
421    o pkg/kpp: replaced _KPP_RL with _RL
422    o bug fixes for vertical diffusivity computations when both KPP and
423        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
424        are no longer updating the vertical diffusivity array
425        (passed as argument) but are (re-) setting those arrays.
426    o pkg/seaice: fix bug in evp solver, while doing that
427      - change (improve?) discretization of stress computations for both
428        cgrid-lsr and evp solver
429      - add a new routine to compute strain rates
430      - the above changes lab_sea results
431      - add no slip conditions for evp solver (off by default), lsr-version
432        may follow
433      - fix exchange for shear at Z-points (does not change lab_sea)
434      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
435        (to force the user to pick a time step since there is not "safe" way
436        of choosing it)
437      - add principal stress diagnostics
438      - rearrange fields for evp a little to avoid having to call a: too many
439        exchanges and b: exchanges for stress trensor components which we do
440        not have.
441      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
442        of evp, complete rewrite for lsr case (latter is does not yet work
443        in all cases)
444    o pkg/kpp: add code to have mixing in shelf ice caverns
445      - add myThid to all kpp routines (long overdue)
446    
447    checkpoint59
448    o pkg/exf:
449      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
450        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
451      - move exf header files from lower_case.h to UPPER_CASE.h ;
452        add missing cvs Header & Name
453      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
454      - add namelist param. selectStressGridPosition, exf_monFreq
455      - retire many _CLIM routines, and remove data.exf_clim
456        + params moved to data.exf
457        + climsst, climsss now handled by exf_set_gen, i.e.
458          climss?period=0 refers to constant field,
459          climss?period=-12 to monthly forcing
460      - split up namelists in data.exf
461    o pkg/seaice:
462      - remove seaice_exch and seaice_exch_uv
463      - remove superfluous exchange of theta
464      - add myThid to seaice_budget_ocean/ice
465      - add new interface for atmospheric wind forcing (C-grid only)
466        + new routine
467        + two new field (taux, tauy for stress over ice)
468        + removed one global field (DAIRN) for C-grid case only
469    o pkg/thsise
470      - 2nd set of modifs for thsice adjoint in conjunction with exf
471    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
472    
473    checkpoint58y_post
474    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
475      vertical diffusivity, similar to that in MOM4; turned on using
476      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
477      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
478    o Added capability for 3D specification of background vertical diffusion
479      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
480      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
481      "data" file that contains the 3D vertical diffusivity coefficients.
482    o ice dynamics (pkg/seaice) with thsice thermodynamics:
483      - add code within pkg thsice to advect & diffuse sea-ice fields
484      similar to (and will replace) what has been added in  seaice_advdiff.F,
485      but: - conserving Mass, Heat & Salt.
486           - better when using non-linear advection scheme (not yet fully tested)
487           - can also be used in atmospheric set-up (for now, only the diffusion).
488    
489    checkpoint58x_post
490    o IO option for global-file compact format:
491      - add options when generating topology (utils/exch2/matlab-topology-generator)
492      - add I/O capability (pkg/mdsio).
493      - adapt utils/matlab/rdmds.m to read this format.
494      for now long-line format not yet supported by pkg/mdsio (& exch2).
495    o shelfice: add a few diagnostics
496    
497    checkpoint58w_post
498    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
499      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
500      (and replace horiVertRatio in NH code).
501      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
502                         and tutorial_plume_on_slope (sensitive to truncation)
503    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
504      directly to drive seaice model (C-grid only)
505    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
506     - reintroduce computation of wind from stress,
507     - compute tau (in exf_bulkformulae.F) from windstress averaged to
508       mass points to avoid tau = 0
509     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
510    o rdmnc.m: make it work with "global" files created with gluemnc
511    o rdmnc.m : some improvements in dealing with singleton dimension
512      (tested on all testreport mnc output files).
513    o genmake2: disable pkg/profiles if netcdf test fails.
514    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
515    o move call to cal_readparms up to make calendar parameters/variable available
516      to all packages
517    
518    checkpoint58v_post
519    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
520      useDynP_inEos_Zc tested.
521    o pkg/exf: changes to properly interpolate/mask/scale initial fields
522    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
523      and portions thereof.  See read_cs.txt for description and examples.
524    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
525      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
526      following the great-circle arc between those 2 points.
527    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
528      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
529    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
530     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
531     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
532     - still needs work (not working with some options ; efficiency to improve)
533       and serious testing.
534     - use this scheme for temperature & salinity in 2 advection test exp.:
535       advect_xy & advect_xz, respectively.
536    
537  checkpoint58u_post  checkpoint58u_post
538  o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.  o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
539  o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.  o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
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